Package org.biopax.paxtools.model

Examples of org.biopax.paxtools.model.Model

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    this.pathways = pathways;
  }

  public void run()
  {
    Model model = main.getOwlModel();

    if (model == null)
    {
      MessageDialog.openError(main.getShell(), "Error!",
        "Load or query a BioPAX model first.");

      return;
    }

    List<String> allNames = new ArrayList<String>(main.getAllPathwayNames());
    Map<String, PathwayHolder> nameToPathwayMap = main.getRootGraph().getNameToPathwayMap();

    assert allNames.size() == nameToPathwayMap.size() : "Sizes do not match!";

    if (allNames.isEmpty())
    {
      String message = model.getObjects().isEmpty() ? "BioPAX model is empty!" :
        "There is no pathway defined in this BioPAX model.\n" +
          "You can create one using \"Pathway > Create\" menu.";

      MessageDialog.openInformation(main.getShell(), "No Pathway!", message);
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        return;
      }

      // Typical merging process
      sources.add(model);
      Model target = main.getOwlModel();

      if (merger == null)
      {
        merger = new Merger(SimpleEditorMap.get(target.getLevel()));
      }
     
      merger.merge(target, sources.toArray(new Model[sources.size()]));

      BioPAXReader reader = new BioPAXReader(target);
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    LocalPathIteration();
  }

  public void LocalPathIteration()
  {
    Model owlModel = this.main.getOwlModel();

        if (owlModel == null)
        {
            MessageDialog.openError(main.getShell(), "Error!",
                "Load or query a BioPAX model first!");
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  private void queryIDs(PathwayCommonsIOHandler ioHandler, List<String> idList) throws IOException
  {
    for (String id : idList)
    {
      ioHandler.setInputIdType(PathwayCommonsIOHandler.ID_TYPE.CPATH_ID);
      Model resultModel = ioHandler.retrieveByID(id);

      if (resultModel != null && !resultModel.getObjects().isEmpty())
      {
        if (main.getOwlModel() != null)
        {
          MergeAction merge = new MergeAction(main, resultModel);
          merge.setOpenPathways(false);
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    main.setRootGraph(root);
  }

  public void run()
  {
    Model model = main.getOwlModel();

    if (model == null)
    {
      MessageDialog.openError(main.getShell(), "Error!",
        "Load or query a BioPAX model first!");
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  private static final String IDBASE = "http://gem.biopax.org/";
  private static final String EXPRESSION = "EXPRESSION";

  public static void writeBioPAX(List<Triplet> trips, String filename) throws Throwable
  {
    Model model = BioPAXLevel.L3.getDefaultFactory().createModel();
    Map<String, BioPAXElement> map = new HashMap<String, BioPAXElement>();

    for (Triplet t : trips)
    {
      createGene(t.M, model, map);
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   */
  private void createGraph(BioPAXGraph root)
  {
    Map<String, NodeModel> map = new HashMap<String, NodeModel>();
   
    Model model = root.getBiopaxModel();

//    for (xref xr : model.getObjects(xref.class))
//    {
//      UniquePrinter.print("xref ["+xr.getID()+"] = ", xr.getDB());
//    }

    if (nestCompartments) createAndNestCompartments(model, map, root);
   
    // Create actors
   
    for (physicalEntity pe : model.getObjects(physicalEntity.class))
    {
      // Complex will be processed later.
      if (pe instanceof complex) continue;

      // Create simple states (Actors)
     
      if (pe.isPHYSICAL_ENTITYof().isEmpty())
      {
        new Actor(root, pe, new ArrayList<physicalEntityParticipant>());
      }
      else
      {
        Collection<List<physicalEntityParticipant>> coll = groupParticipants(pe);
       
        for (List<physicalEntityParticipant> list : coll)
        {
          CompoundModel compart = getCompartment(list.get(0), map, root);
         
          Actor actor = new Actor(compart, pe, list);
         
          for (physicalEntityParticipant par : list)
          {
            map.put(par.getRDFId(), actor);
          }
        }
      }
    }
   
    // Create complexes

    for (complex cmp : model.getObjects(complex.class))
    {
      if (cmp.isPHYSICAL_ENTITYof().isEmpty())
      {
        Complex c = new Complex(root, cmp, new ArrayList<physicalEntityParticipant>(0));
        createComplexContent(c, cmp, new ArrayList<physicalEntityParticipant>());
      }
      else
      {
        Collection<List<physicalEntityParticipant>> coll = groupParticipants(cmp);
       
        for (List<physicalEntityParticipant> list : coll)
        {
          CompoundModel compart = getCompartment(list.get(0), map, root);

          if (compart == root)
          {
            String nm = Complex.suggestCompartmentNameUsingMembers(cmp.getCOMPONENTS());

            if (nm != null)
            {
              if (nestCompartments) nm = CompartmentManager.getUnifiedName(nm);
              compart = getCompartment(nm, map, root);
            }
          }

          NodeModel nd;

          if (cmp.getCOMPONENTS().isEmpty())
          {
            nd = new Actor(compart, cmp, list);
          }
          else
          {
            Complex c = new Complex(compart, cmp, list);
            createComplexContent(c, cmp, list);
            nd = c;
          }

          for (physicalEntityParticipant par : list)
          {
            map.put(par.getRDFId(), nd);
          }
        }
      }
    }   
   
    // Create events
   
    for (conversion conv : model.getObjects(conversion.class))
    {
      String compName = Conversion.getPossibleCompartmentName(conv);

      if (compName != null && nestCompartments)
        compName = CompartmentManager.getUnifiedName(compName);
     
      CompoundModel compart = compName == null ? root : (CompoundModel) map.get(compName);
     
      Conversion forwd = null, rever = null;
     
      if (evidenceExists(conv, Conversion.LEFT_TO_RIGHT))
      {
        forwd = new Conversion(compart, conv, Conversion.LEFT_TO_RIGHT, map);
        forwd.selectBestCompartment();
      }     
      if (evidenceExists(conv, Conversion.RIGHT_TO_LEFT))
      {
        rever = new Conversion(compart, conv, Conversion.RIGHT_TO_LEFT, map);
        rever.selectBestCompartment();
      }
      if (forwd == null && rever == null)
      {
        forwd = new Conversion(compart, conv, Conversion.LEFT_TO_RIGHT, map);
        forwd.selectBestCompartment();
      }
    }

    for (interaction inter : model.getObjects(interaction.class))
    {
      boolean drawPPI = true;
      if (!drawPPI) break;

      if (!(inter instanceof conversion) && !(inter instanceof control))
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    this.ruleTypes = new ArrayList<BinaryInteractionType>();
  }

  public void run()
  {
    Model model = main.getOwlModel();

    if (model == null)
    {
      return;
    }
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    this.pathways = pathways;
  }

  public void run()
  {
    Model model = main.getOwlModel();

    if (model == null)
    {
      MessageDialog.openError(main.getShell(), "Error!",
        "Load or query a BioPAX model first.");

      return;
    }

    List<String> allNames = new ArrayList<String>(main.getAllPathwayNames());
    Map<String, pathway> nameToPathwayMap = new HashMap<String, pathway>();

    for (pathway p : model.getObjects(pathway.class))
    {
      if (!p.getPATHWAY_COMPONENTS().isEmpty())
      {
        nameToPathwayMap.put(p.getNAME(), p);
      }
    }

    assert allNames.size() == nameToPathwayMap.size() : "Sizes do not match!";

    if (allNames.isEmpty())
    {
      String message = model.getObjects().isEmpty() ? "BioPAX model is empty!" :
        "There is no pathway defined in this BioPAX model.\n" +
          "You can create one using \"Pathway > Create\" menu.";

      MessageDialog.openInformation(main.getShell(), "No Pathway!", message);
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        return;
      }

      // Typical merging process
      sources.add(model);
      Model target = main.getOwlModel();

      if (merger == null)
      {
        merger = new Merger(new JenaEditorMap(BioPAXLevel.L2));
      }
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Related Classes of org.biopax.paxtools.model.Model

  • gem.BioPAXWriter
  • org.gvt.action.DeletePathwayAction
  • org.gvt.action.ExportToSIFAction
  • org.gvt.action.LocalCommonStreamQueryAction
  • org.gvt.action.LocalCompartmentQueryAction
  • org.gvt.action.LocalGoIQueryAction
  • org.gvt.action.LocalNeighborhoodQueryAction
  • org.gvt.action.LocalPathIterationQueryAction
  • org.gvt.action.LocalPoIQueryAction
  • org.gvt.action.MergeAction
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